I haven't found a way so far to boot Windows 2000 with lilo and I don't think it works for grub either because it seems to me that win2k heavily depends on its own bootmanager.
First of all you have to repair it. Make a linux bootdisk before or you won't be able to boot to linux then! Use the bootable win2k CD and go to the repair console. with "help" you should get the commands for repearing the MBR but you should better google for it before. I've done this once and never again because I was happy that I didn't have to reinstall
You can then tell the C:\boot.ini to add an option for Linux to the windows boot manager.
To do so you have to go into linux with the bootdisk and configure the bootmanager to a Linux only system and install it on the linux *partition* not in the MBR, or you have to start again
dd if=/dev/hda2 of=/mnt/bootsect.lnx bs=512 count=1
change the pathes to the according directories on your PC. Windows has to read the 2nd one!
Boot into windows and copy the bootsect.lnx to C:\ and edit the boot.ini and add
under [operating systems].
Then you can boot Linux from the windows boot manager.
BUT there are a few concerns.
a) it's a hassle when you update your bootmanager often, for test purposes for instances.
b) do something wrong and you have to repair the MBR again.
c) I have done this only in Lilo. So if you choose this way then I strongly suggest to google for it.
d) to avoid trouble I put lilo on a boot disk. So it's floppy-in="boot Linux" and floppy-out="boot Win2k" for me. It's easier to update linux and the windows bootmanager doesn't have to be touched.